CRiSM
A Python CLI connecting marker-gene discovery and extraction from genomes with alignment, sequence concatenation, and phylogenetic inference.
Installation
The source installation in the README (Conda environment) is the documented route; a stable PyPI release is not assumed.
Status
Invocation, failure handling and marker-alignment validation are implemented. Nine smoke tests passed locally and in Linux CI on October 3, 2026. Installed CLI execution was checked; the complete phylogenetic workflow with external tools remains unvalidated.